Consumers demand high quality and low price when purchasing goods such as dairy and meat products. However, many consumers also want assurance that the products and production systems are managed to minimise risk and maximise benefits to human health, while also being non-detrimental to the environment and to the welfare of animals.
It is well known that the genetics of an animal has a substantial impact on production and product quality, and on health, environmental and animal welfare issues. The ability to determine a phenotype of an animal by using a genetic test is a valuable tool for achieving rapid identification of animals and animal products with beneficial characteristics and for forming a group of animals having enhanced production and/or product quality. Animals can be grouped based on genetic differences that relate to animal or animal product traits that are of economic interest. In the case of the dairy industry, examples of important traits are milk production, milk protein content, fat production, and specific components of milk that are associated with health, for example the absence of the β-casein A1 protein or the percentage of saturated fats.
In a typical genetic test, the DNA sequence of a gene encoding a protein or group of proteins related to a physical trait of interest will be known. A DNA sample is obtained from an animal and a combination of polymerase chain reaction (PCR) amplification, DNA fragment analysis, and data processing is used to identify the DNA present at the known location for the gene in the animal's genome. Highly automated testing enables the presence of a gene or gene variant, and therefore the ability to exhibit a physical trait, to be determined for a large number of animals comparatively quickly and efficiently.
The gene that is responsible for a particular physical trait of an animal may be identifiable by a single nucleotide polymorphism (SNP). An SNP is a DNA sequence at a location in an animal's genome which is different to the DNA sequence at the same location in the genome of another animal by virtue of only one nucleotide. Even a difference as small as this can mean an animal exhibits a particular physical trait whereas another animal does not.
One example of the significance of an SNP is the genetic makeup of a bovine cow that enables the production of β-casein proteins in its milk. Typically, a cow will produce β-caseins in its milk. However, several β-casein variants are known including A1, A2, A3, B, C, D, E, and F. One difference between the A2, A3, D, E, and F variants on the one hand and the A1, B, and C variants on the other hand is that the former group has a proline residue at position 67 of the β-casein protein whereas the latter group has a histidine residue at position 67. This difference is determined by substitution of the nucleotide adenine with the nucleotide cytosine at position 200 of the coding region of the β-casein gene. It is therefore possible to distinguish between the two groups of β-casein variants by identifying and testing for the SNP that encodes for the β-casein protein of an animal.
There are a number of reports indicating that the presence of β-casein A1 in the human diet is linked with the incidence of certain diseases, specifically diabetes (Elliott, R. B., Harris, D. P., Hill, J. P., Bibby, N. J., Wasmuth, H. E., Type I (Insulin-Dependent) Diabetes Mellitus and Cow Milk: Casein Variant Consumption, Diabetologia 1999; 42:292-6; Wasmuth, H. E., Rosenbauer, J., Elliot, R. B., McLachlan, C., Erhardt, G., Giani, G., Kolb, H., β-Casein A1 Consumption and Incidence of Type 1 Diabetes in Germany. Kongress der Europäischen Diabetesgesellschaft vom 28.-30. Sep. 1999 in Brüssels/Belgium. Proceedings published in Diabetologia 42 (Suppl. 1): A88; 1999) and coronary heart disease (McLachlan, C. N. (2001) β-casein A1, Ischaemic Heart Disease Mortality, and Other Illnesses. Med. Hypotheses 56(2):262-72).
In addition to phenotyping a cow by identifying the particular β-casein variant or variants produced in the cow's milk, it is well known to genotype a cow by identifying the SNP it possesses to gain knowledge of whether the cow has the ability to produce a certain β-casein variant. A method of selecting bovine cows on the basis of such genotyping to form milking herds which will produce milk free of the β-casein A1 variant, and preferably solely the β-casein A2 variant, is described in PCT/NZ96/00039 (published as WO 96/36239).
Studies have shown that SNPs, or other DNA variants (tandem repeats, insertion-deletions) are valuable in predicting a disease, the quality of an animal product, or a production benefit. However, in cases where genetic selection is used to sort, cull or mate animals, a selection strategy based on the use of a single SNP or trait is sub-optimal. This is because an SNP, such as an SNP within the β-casein gene, is not randomly associated with the surrounding DNA. The region of DNA that surrounds the genotyped SNP may encode one or more functions which also influence a physical trait. Selection based on a single SNP may therefore inadvertently select for traits additional to the trait of interest.
The inventors have now found that it is possible to determine whether a bovine animal possesses a gene for the β-casein A1 protein or a gene for the β-casein A2 protein, not by identifying the DNA of that gene, but by identifying SNPs or haplotypes (combinations of SNPs) in the region of the animal's genome where the gene for β-casein is located.
It is therefore an object of the invention to provide a novel method of genotyping an animal for its β-casein gene, or to at least provide a useful alternative to known methods.